Abstract

Background

Large scale genome-wide association studies have become popular since the introduction
of high throughput genotyping platforms. Efficient management of the vast array of
data generated poses many challenges.

Description

We have developed an open source web-based data management system for the large amount
of genotype data generated from the Affymetrix GeneChip® Mapping Array and Affymetrix Genome-Wide Human SNP Array platforms. The database supports
genotype calling using DM, BRLMM, BRLMM-P or Birdseed algorithms provided by the Affymetrix
Power Tools. The genotype and corresponding pedigree data are stored in a relational
database for efficient downstream data manipulation and analysis, such as calculation
of allele and genotype frequencies, sample identity checking, and export of genotype
data in various file formats for analysis using commonly-available software. A novel
method for genotyping error estimation is implemented using linkage disequilibrium
information from the HapMap project. All functionalities are accessible via a web-based
user interface.

Conclusion

OpenADAM provides an open source database system for management of Affymetrix genome-wide
association SNP data.